rs1209921

Variant names:

• chr21-38784351-G-C
• rs1209921
• ENST00000785403.1:n.449-2006G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000785403.1(ENSG00000302272):​n.449-2006G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,120 control chromosomes in the GnomAD database, including 29,184 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.60 (29184 hom., cov: 33)
• Consequence: ENSG00000302272 ENST00000785403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 2 publications found

Genes affected

ENSG00000302272 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985480	XR_001755102.2	n.40+260G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302272	ENST00000785403.1	n.449-2006G>C		intron_variant	Intron 3 of 3
ENSG00000302272	ENST00000785404.1	n.307-2006G>C		intron_variant	Intron 2 of 2
ENSG00000302272	ENST00000785405.1	n.356+260G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91184 AN: 152002 Hom.: 29181 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.598

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.600 AC: 91219 AN: 152120 Hom.: 29184 Cov.: 33 AF XY: 0.602 AC XY: 44738 AN XY: 74356

African (AFR) AF: 0.366 AC: 15181 AN: 41456

American (AMR) AF: 0.672 AC: 10269 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2308 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2641 AN: 5178

South Asian (SAS) AF: 0.583 AC: 2812 AN: 4822

European-Finnish (FIN) AF: 0.754 AC: 7980 AN: 10584

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47948 AN: 68002

Other (OTH) AF: 0.597 AC: 1263 AN: 2114

Alfa AF: 0.647 Hom.: 4103

Bravo AF: 0.584

Asia WGS AF: 0.538 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.55
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1209921; hg19: chr21-40156275;